BioC 3.3: CHECK report for BiGGR on windows2.bioconductor.org
This page was generated on 2015-10-27 12:15:22 -0400 (Tue, 27 Oct 2015).
BiGGR 1.7.0 Anand K. Gavai , Hannes Hettling
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/BiGGR | Last Changed Rev: 109592 / Revision: 109948 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: BiGGR
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Version: 1.7.0
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Command: rm -rf BiGGR.buildbin-libdir BiGGR.Rcheck && mkdir BiGGR.buildbin-libdir BiGGR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiGGR.buildbin-libdir BiGGR_1.7.0.tar.gz >BiGGR.Rcheck\00install.out 2>&1 && cp BiGGR.Rcheck\00install.out BiGGR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BiGGR.buildbin-libdir --install="check:BiGGR-install.out" --force-multiarch --no-vignettes --timings BiGGR_1.7.0.tar.gz
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StartedAt: 2015-10-27 00:49:50 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 00:58:30 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 520.0 seconds
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RetCode: 0
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Status: OK
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CheckDir: BiGGR.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf BiGGR.buildbin-libdir BiGGR.Rcheck && mkdir BiGGR.buildbin-libdir BiGGR.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BiGGR.buildbin-libdir BiGGR_1.7.0.tar.gz >BiGGR.Rcheck\00install.out 2>&1 && cp BiGGR.Rcheck\00install.out BiGGR-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=BiGGR.buildbin-libdir --install="check:BiGGR-install.out" --force-multiarch --no-vignettes --timings BiGGR_1.7.0.tar.gz
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/BiGGR.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiGGR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BiGGR' version '1.7.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BiGGR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: 'stringr'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gprMapping: no visible global function definition for 'str_detect'
sampleFluxEnsemble: no visible global function definition for 'Xsample'
sampleFluxEnsemble: no visible global function definition for 'xsample'
sbml2hyperdraw: no visible global function definition for 'graphLayout'
sbml2hyperdraw: no visible global function definition for
'nodeDataDefaults<-'
sbml2hyperdraw: no visible global function definition for
'edgeDataDefaults<-'
sbml2hyperdraw: no visible global function definition for
'graphDataDefaults<-'
sbml2hyperdraw : <anonymous>: no visible global function definition for
'edgeData<-'
Undefined global functions or variables:
Xsample edgeData<- edgeDataDefaults<- graphDataDefaults<- graphLayout
nodeDataDefaults<- str_detect xsample
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [212s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gprMapping 155.79 0.05 155.84
gprMappingAvg 15.75 0.03 15.78
buildSBMLFromGenes 5.96 0.25 6.22
** running examples for arch 'x64' ... [220s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
gprMapping 160.56 0.05 160.61
gprMappingAvg 16.05 0.00 16.06
buildSBMLFromGenes 5.98 0.34 6.33
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'c:/biocbld/bbs-3.3-bioc/meat/BiGGR.Rcheck/00check.log'
for details.
BiGGR.Rcheck/00install.out:
install for i386
* installing *source* package 'BiGGR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'BiGGR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiGGR' as BiGGR_1.7.0.zip
* DONE (BiGGR)
BiGGR.Rcheck/examples_i386/BiGGR-Ex.timings:
name | user | system | elapsed
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BiGGR-package | 2.78 | 0.08 | 3.01 |
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E.coli_iAF1260 | 0.84 | 0.06 | 0.91 |
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E.coli_iJR904 | 0.54 | 0.01 | 0.55 |
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E.coli_textbook | 0.03 | 0.13 | 0.15 |
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H.pylori_ilT341 | 0.20 | 0.05 | 0.25 |
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H.sapiens_Recon1 | 1.00 | 0.09 | 1.10 |
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M.barkeri_iAF692 | 0.22 | 0.16 | 0.37 |
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M.tuberculosis_iNJ661 | 0.25 | 0.09 | 0.34 |
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P.putida_iJN746 | 0.26 | 0.08 | 0.35 |
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Recon2 | 2.00 | 0.08 | 2.08 |
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S.aureus_iSB619 | 0.23 | 0.07 | 0.31 |
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S.cerevisiae_iND750 | 0.41 | 0.02 | 0.43 |
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buildSBMLFromBiGG | 0.13 | 0.00 | 0.12 |
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buildSBMLFromGenes | 5.96 | 0.25 | 6.22 |
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buildSBMLFromPathways | 4.60 | 0.05 | 4.64 |
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buildSBMLFromReactionIDs | 1.90 | 0.00 | 1.91 |
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createLIMFromBiGG | 0.10 | 0.00 | 0.09 |
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createLIMFromSBML | 1.09 | 0.06 | 1.16 |
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extractGeneAssociations | 2.10 | 0.01 | 2.11 |
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extractPathways | 2.78 | 0.00 | 2.78 |
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getPathwaysForSBML | 2.47 | 0.00 | 2.47 |
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getRates | 0 | 0 | 0 |
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gprMapping | 155.79 | 0.05 | 155.84 |
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gprMappingAvg | 15.75 | 0.03 | 15.78 |
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lying.tunell.data | 0 | 0 | 0 |
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rmvSpliceVariant | 2.08 | 0.00 | 2.08 |
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sampleFluxEnsemble | 2.64 | 0.36 | 3.03 |
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sbml2hyperdraw | 2.59 | 0.00 | 2.59 |
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BiGGR.Rcheck/examples_x64/BiGGR-Ex.timings:
name | user | system | elapsed
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BiGGR-package | 3.38 | 0.08 | 3.45 |
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E.coli_iAF1260 | 0.92 | 0.07 | 1.00 |
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E.coli_iJR904 | 0.42 | 0.00 | 0.43 |
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E.coli_textbook | 0.05 | 0.05 | 0.09 |
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H.pylori_ilT341 | 0.28 | 0.02 | 0.30 |
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H.sapiens_Recon1 | 1.70 | 0.04 | 1.75 |
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M.barkeri_iAF692 | 0.32 | 0.10 | 0.40 |
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M.tuberculosis_iNJ661 | 0.43 | 0.12 | 0.57 |
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P.putida_iJN746 | 0.38 | 0.08 | 0.45 |
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Recon2 | 2.50 | 0.08 | 2.58 |
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S.aureus_iSB619 | 0.33 | 0.03 | 0.36 |
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S.cerevisiae_iND750 | 0.45 | 0.08 | 0.53 |
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buildSBMLFromBiGG | 0.14 | 0.00 | 0.14 |
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buildSBMLFromGenes | 5.98 | 0.34 | 6.33 |
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buildSBMLFromPathways | 4.32 | 0.03 | 4.34 |
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buildSBMLFromReactionIDs | 1.76 | 0.03 | 1.80 |
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createLIMFromBiGG | 0.11 | 0.00 | 0.11 |
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createLIMFromSBML | 1.33 | 0.05 | 1.38 |
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extractGeneAssociations | 2.03 | 0.00 | 2.03 |
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extractPathways | 2 | 0 | 2 |
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getPathwaysForSBML | 2.6 | 0.0 | 2.6 |
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getRates | 0 | 0 | 0 |
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gprMapping | 160.56 | 0.05 | 160.61 |
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gprMappingAvg | 16.05 | 0.00 | 16.06 |
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lying.tunell.data | 0 | 0 | 0 |
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rmvSpliceVariant | 2.78 | 0.00 | 2.79 |
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sampleFluxEnsemble | 3.27 | 0.44 | 3.70 |
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sbml2hyperdraw | 2.75 | 0.00 | 2.75 |
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